com {bio3d}

Center of Mass

Description

Calculate the center of mass of a PDB object.

Usage

com(...)

## S3 method for class 'pdb'
com(pdb, inds=NULL, use.mass=TRUE, ...)

## S3 method for class 'xyz'
com(xyz, mass=NULL, ...)

Arguments

pdb

an object of class pdb as obtained from function read.pdb.

inds

atom and xyz coordinate indices obtained from atom.select that selects the elements of pdb upon which the calculation should be based.

use.mass

logical, if TRUE the calculation will be mass weighted (center of mass).

...

additional arguments to atom2mass.

xyz

a numeric vector or matrix of Cartesian coordinates (e.g. an object of type xyz).

mass

a numeric vector containing the masses of each atom in xyz.

Details

This function calculates the center of mass of the provided PDB structure / Cartesian coordiantes. Atom names found in standard amino acids in the PDB are mapped to atom elements and their corresponding relative atomic masses.

In the case of an unknown atom name elety.custom and mass.custom can be used to map an atom to the correct atomic mass. See examples for more details.

Alternatively, the atom name will be mapped automatically to the element corresponding to the first character of the atom name. Atom names starting with character H will be mapped to hydrogen atoms.

Value

Returns the Cartesian coordinates at the center of mass.

Author(s)

Lars Skjaerven

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

read.pdb, atom2mass

Examples

# PDB server connection required - testing excluded

## Stucture of PKA:
pdb <- read.pdb("3dnd")

## Center of mass:
com(pdb)

## Center of mass of a selection
inds <- atom.select(pdb, chain="I")
com(pdb, inds)

## using XYZ Cartesian coordinates
xyz <- pdb$xyz[, inds$xyz]
com.xyz(xyz)

## with mass weighting
com.xyz(xyz, mass=atom2mass(pdb$atom[inds$atom, "elety"]) )



## Not run: 
## Unknown atom names
pdb <- read.pdb("3dnd")
inds <- atom.select(pdb, resid="LL2")
mycom <- com(pdb, inds, rescue=TRUE)
#warnings()


## Map atom names manually
pdb <- read.pdb("3RE0")
inds <- atom.select(pdb, resno=201)

myelety  <- data.frame(name = c("CL2","PT1","N1","N2"), symb = c("Cl","Pt","N","N"))
mymasses <- data.frame(symb = c("Cl","Pt"), mass = c(35.45, 195.08))
mycom    <- com(pdb, inds, elety.custom=myelety, mass.custom=mymasses)

## End(Not run)